[gmx-users] Thermodynamic integration

[Mark Abraham]

Hi,

Also you might consider pmx
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
generation. There is further work in the pipeline, so do get in touch with
Bert if there's something of interest.

Mark

On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> From the site, “..or the free energy of a mutation of a side chain.”
>
> I think this is what I am after. Many thanks for the link.
>
> Anthony
>
>
>
> On 18/04/2016 10:42, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
> behalf of Hannes Loeffler"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> Hannes.Loeffler at stfc.ac.uk> wrote:
>
> >A good starting point is http://www.alchemistry.org/ which has quite a
> >lot of detail on relative alchemical free energy simulations (not only
> >TI).
> >
> >On Mon, 18 Apr 2016 09:27:02 +0000
> >"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
> >
> >> Hi all,
> >>
> >> I¹m looking for a guide on performing TI between a protein in its
> >> crystal periodicity with a particular residue (state A), to the same
> >> system but with a different residue (state B).
> >>
> >> I¹m currently using
> >>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/fr
> >>ee
> >> _energy/01_theory.html as a guide, however this is more, if I
> >> understand having read through it, on the presence-to-absence of
> >> methane in a water solvent rather than a replacement with something
> >> else.
> >>
> >> I haven¹t had too much luck googling and I¹m looking piecemeal
> >> through the manual with little success.
> >>
> >> Thanks
> >> Anthony
> >>
> >>
> >>
> >
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.